title: top1 top2 rrm3 1

city: New York

first: Duncan

last: Smith

state: NY

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

data_processing:
bowtie2 v.2.2.9 was used to align FASTQ files to the S. cerevisiae reference genome (SGD, R64-2-1,). samtools (1.3.1) was used to sort and select reads with MAPQ score ≥40. BEDPE/BED files were generated using bedtools v.2.26.0; bedtools genomecov was used to calculate Watson and Crick read-depth with 1-based coordinates.
Genome_build: S. cerevisiae S288C, build R64-2-1, released 18 Nov 2014
Supplementary_files_format_and_content: BED files are headerless text files that contain the following tab-delimited columns: chromosome, 5'-position, 3'-position, read identifier, MAPQ score, and strand.
BEDPE files are headerless text files that contain the following tab-delimited columns: mate1 chromosome, mate1 5'-position, mate1 3'-position, mate2 chromosome, mate2 5'-position, mate2 3'-position, mate1 read identifier, MAPQ score, mate1 strand, mate2 strand
pw.g.txt files are headerless text files that contain the following tab-delimited columns: chromosome, base, fraction of Watson reads

organism: Saccharomyces cerevisiae

growth_protocol: Asynchronous cultures were grown to log phase at 30C in YPD before a 2.5h treatment with 40ug/mL doxycyclin to deplete DNA ligase. Strains with FRB-tagged proteins were treated with 1ug/mL rapamycin for 1h after reaching log phase but before ligase depletion.

extract_protocol:
Okazaki fragments were enriched by sequential elutions from ion exchange columns as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).
Libraries were constructed as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438) with the following changes: after adaptor ligation, samples were cleaned using a PCR purification kit (GeneJET, ThermoFisher) instead of S-300 columns, and second-strand synthesis was carried out by Taq polymerase (NEB) at 50C. Libraries were purified using magnetic beads (HighPrep PCR Clean-up, MagBio) before and after amplification.

tag: lab strain

value: W303 tor1-1::HIS3, fpr1Δ::NatMX4, RPL13A-2xFKBP12::TRP1, cdc9::tetO7-CDC9 cmv_LacI-URA3

tag: molecule subtype

value: DNA, Okazaki fragments


title: top1 top2 rrm3 2

status: Public on Nov 02 2019

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

tag: strain background

tag: genotype/variation


title: NB3_AS601245_C1D3_rep2_6h

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

library_source: transcriptomic

data_processing:
Illumina Sequencing by HiSeq3000
Sequenced reads were quality-controlled, trimmed for adaptor sequences (if present), then mapped to the ENSEMBL GRCh38 reference genome using STAR v 2.6.0a
Uniquely-mapped reads aligned to exons were counted by HTSeq v.0.6.1.
The raw read counts were normalized by the DESeq2 R package v.3.4.4
Genome_build: GRCh38 (ftp://ftp.ensembl.org/pub/release-92/fasta/homo_sapiens/dna/), downloaded on July 2nd, 2018.
Supplementary_files_format_and_content: Tab-delimited text files include raw counts of sequencing reads for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Neural crest-derived cells

growth_protocol: Cells were cultured in 3 parts DMEM Low glucose, pyruvate GlutaMax medium (ThermoFisher, cat. 21885-025) and 1 part Ham’s F12 Nutrient Mix (ThermoFisher, cat. 31765-027), supplemented with 10% B-27 (ThermoFisher, cat. 17504044) and 1% penicillin-streptomycin mix.

extract_protocol:
After the treatment, the drug-containing medium was removed and the plates were snap frozen on dry ice. RNA isolation and cDNA synthesis were performed by the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio USA), as per the manufacturer's instructions.
RNA libraries were prepared for sequencing using the SMART-Seq2 method.

treatment_protocol: Cells were seeded in 384-well plates (1500 cells/well) and treated with 13 different chemical componds (3 doses and 4 replicates each).

tag: cell type

value: Human-derived xenograft neuroblastoma (NB) primary cells

tag: passages

value: Child

tag: cell line id

tag: chemical compound

tag: time point


title: top2 rrm3 3

value: TOP2-FRB::HygMX6 rrm3{delta}::HygMX6


title: top2 rrm3 2


title: top2 rrm3 1


title: NB2_Fasudil_C4D3_rep3_6h

value: Fasudil


title: top1 rrm3 3

source_name: top1Δ ;rrm3Δ


title: NB3_AZDS438_C2D1_rep2_6h


title: NB3_AZDS438_C2D2_rep2_6h


title: NB3_Fasudil_C4D1_rep2_6h


title: NB3_DL-PDMP_C3D1_rep2_6h

value: DL-PDMP


title: NB3_DL-PDMP_C3D2_rep2_6h


title: NB3_Fasudil_C4D2_rep2_6h


title: brn1 rrm3 2


title: NB3_Fasudil_C4D3_rep2_6h


title: rad18 rrm3 3

value: W303 cdc9::tetO7-CDC9 cmv_LacI-NatMX4


title: top1 rrm3 2


title: NB3_DL-PDMP_C3D3_rep2_6h


title: top1 rrm3 1


title: NB3_AZDS438_C2D3_rep2_6h


title: top1 top2 rrm3 3


title: brn1 rrm3 1


title: brn1 rrm3 2 tech rep

value: DS776, technical replicate


title: NB3_DMSO1_DMSO1_rep6_6h

value: DMSO


title: NB2_DMSO2_DMSO2_rep4_6h


title: rad18 rrm3 1


title: NB2_Torin 2_C13D3_rep2_6h

value: Torin 2


title: NB2_AS601245_C1D1_rep3_6h


title: NB2_AS601245_C1D2_rep3_6h


title: NB2_Torin 2_C13D2_rep2_6h


title: anchor away 2

source_name: anchor away; CDC9 degron

value: anchor away background


title: NB2_Torin 2_C13D1_rep2_6h


title: anchor away 3


title: TLS rrm3 1

source_name: rev1Δ;rev3Δ;rad30Δ ;rrm3Δ

value: rev1{delta}::HygMX6; rev3{delta}::KanMX6; rad30{delta}::LEU2; rrm3{delta}::HygMX6


title: TLS rrm3 3


title: rad18 rrm3 2


title: bdp1 rrm3 2

value: BDP1-FRB::HygMX6; rrm3{delta}::HygMX6


title: bdp1 rrm3 1


title: bdp1 rrm3 3


title: NB2_Rosiglitazone_C12D3_rep2_6h

value: Rosiglitazone


title: rpc25 rpc82 rrm3 2


title: NB2_Rosiglitazone_C12D1_rep2_6h


title: NB2_Rosiglitazone_C12D2_rep2_6h


title: NB2_Control_CTR_rep8_6h

value: Control


title: rpc25 rrm3 3

value: RPC25-FRB::HygMX6; rrm3{delta}::HygMX6


title: NB2_Retinoic acid_C11D2_rep2_6h

value: Retinoic acid


title: rpc25 rpc82 rrm3 3

value: W303 tor1-1::HIS3, fpr1Δ::NatMX4, RPL13A-2xFKBP12::TRP1, cdc9::tetO7-CDC9 cmv_LacI-URA3

value: DNA, Okazaki fragments


title: NB3_Control_CTR_rep7_6h

value: Human-derived xenograft neuroblastoma (NB) primary cells

value: Child


title: rrm3 AA 3


title: rpc25 rpc82 rrm3 1


title: NB3_GW405833_C5D1_rep2_6h


title: NB3_JQ1_C6D1_rep2_6h


title: NB3_GW405833_C5D3_rep2_6h


title: NB2_Retinoic acid_C11D3_rep2_6h


title: NB3_GW405833_C5D2_rep2_6h


title: rpc25 rrm3 2

value: RPC25-FRB::KanMX6; rrm3{delta}::HygMX6


title: rrm3 AA 1


title: rrm3 AA 2


title: TLS rrm3 2


title: rpc25 rrm3 1


title: NB3_Lovastatin_C7D2_rep2_6h

value: Lovastatin


title: NB3_Lovastatin_C7D1_rep2_6h


title: NB3_JQ1_C6D2_rep2_6h


title: NB3_JQ1_C6D3_rep2_6h


title: NB3_Lovastatin_C7D3_rep2_6h


title: NB3_DMSO2_DMSO2_rep6_6h


title: NB2_DMSO1_DMSO1_rep4_6h


title: NB2_PK11195_C10D1_rep2_6h


title: NB2_PK11195_C10D2_rep2_6h


title: NB3_Omiplasib_C8D1_rep2_6h

value: Omiplasib


title: NB2_PK11195_C10D3_rep2_6h


title: NB2_Retinoic acid_C11D1_rep2_6h


title: NB2_Palbociclib_C9D3_rep2_6h

value: Palbociclib


title: NB2_Palbociclib_C9D2_rep2_6h


title: NB2_Omiplasib_C8D1_rep2_6h


title: NB2_Control_CTR_rep7_6h


title: NB3_Omiplasib_C8D3_rep2_6h


title: NB2_Palbociclib_C9D1_rep2_6h


title: NB3_Omiplasib_C8D2_rep2_6h


title: NB3_Control_CTR_rep6_6h


title: NB2_Omiplasib_C8D2_rep2_6h


title: NB3_Palbociclib_C9D2_rep2_6h


title: NB3_Palbociclib_C9D3_rep2_6h


title: NB2_Omiplasib_C8D3_rep2_6h


title: NB3_PK11195_C10D2_rep2_6h


title: NB3_Retinoic acid_C11D1_rep2_6h


title: NB3_Retinoic acid_C11D2_rep2_6h


title: NB2_Lovastatin_C7D3_rep2_6h


title: NB3_PK11195_C10D1_rep2_6h


title: NB2_DMSO2_DMSO2_rep3_6h

value: DMSO


title: NB3_DMSO1_DMSO1_rep5_6h


title: NB3_PK11195_C10D3_rep2_6h


title: NB2_Lovastatin_C7D2_rep2_6h


title: NB2_Lovastatin_C7D1_rep2_6h


title: NB2_JQ1_C6D3_rep2_6h


title: NB2_JQ1_C6D2_rep2_6h


title: NB2_GW405833_C5D2_rep2_6h


title: NB3_Palbociclib_C9D1_rep2_6h


title: NB2_GW405833_C5D1_rep2_6h


title: NB2_JQ1_C6D1_rep2_6h


title: NB2_Fasudil_C4D3_rep2_6h

value: Fasudil


title: NB2_GW405833_C5D3_rep2_6h


title: NB2_Control_CTR_rep6_6h


title: NB3_Retinoic acid_C11D3_rep2_6h


title: NB3_Control_CTR_rep5_6h


title: NB3_Rosiglitazone_C12D1_rep2_6h


title: NB3_Torin 2_C13D2_rep2_6h

value: Torin 2


title: NB3_Torin 2_C13D1_rep2_6h


title: NB3_Rosiglitazone_C12D3_rep2_6h


title: NB3_AS601245_C1D2_rep1_6h


title: NB3_AS601245_C1D1_rep1_6h


title: NB3_Torin 2_C13D3_rep2_6h


title: NB3_DMSO2_DMSO2_rep5_6h


title: NB3_AS601245_C1D3_rep1_6h


title: NB2_Fasudil_C4D2_rep2_6h


title: NB2_DL-PDMP_C3D3_rep2_6h

value: DL-PDMP


title: NB2_DMSO1_DMSO1_rep3_6h


title: anchor away 1

value: anchor away background


title: NB2_DL-PDMP_C3D2_rep2_6h


title: NB2_AZDS438_C2D3_rep2_6h


title: NB2_Fasudil_C4D1_rep2_6h


title: NB2_DL-PDMP_C3D1_rep2_6h


title: NB2_AZDS438_C2D2_rep2_6h


title: NB2_AZDS438_C2D1_rep2_6h


title: NB2_AS601245_C1D2_rep2_6h


title: NB2_Control_CTR_rep5_6h


title: NB2_AS601245_C1D3_rep2_6h


title: NB3_Control_CTR_rep4_6h


title: NB3_Rosiglitazone_C12D2_rep2_6h

value: Rosiglitazone


title: NB3_DL-PDMP_C3D1_rep1_6h


title: NB3_AZDS438_C2D1_rep1_6h


title: NB3_AZDS438_C2D3_rep1_6h


title: NB3_AZDS438_C2D2_rep1_6h


title: NB3_Fasudil_C4D3_rep1_6h


title: NB3_DL-PDMP_C3D3_rep1_6h


title: NB3_Fasudil_C4D2_rep1_6h


title: NB3_Fasudil_C4D1_rep1_6h


title: NB2_AS601245_C1D1_rep2_6h


title: NB3_DMSO1_DMSO1_rep4_6h


title: NB2_Torin 2_C13D1_rep1_6h


title: NB3_DL-PDMP_C3D2_rep1_6h


title: NB2_Rosiglitazone_C12D3_rep1_6h


title: NB2_Torin 2_C13D3_rep1_6h


title: NB2_Torin 2_C13D2_rep1_6h


title: injured_wt_10X_18_016

city: Stockholm

first: Margherita

last: Zamboni

address: Solnavägen 9

department: Cell and Molecular Biology

institute: Karolinska Institutet

description:
WT astrocytes in SWI
10X_18_016

data_processing:
bcl files were converted to fastq files using cellranger mkfastq (v2.0.1)
Alignment and filtering was performed with cellranger count (v2.0.1)
Samples were integrated in a single Seurat object and initial filtering was performed to exclude genes expressed in < 3 cells and cells with < 200 detected genes
Further selection of high quality cells and exclusion of contaminating cells was performed based on cell type markers and detection of tdTomato transcripts
Genome_build: mm10 supplemented with tdTomato DNA sequence
Supplementary_files_format_and_content: csv files contain raw gene expression matrices (all_cells_10X_gbm.csv encompasses all cortical cells from the experiment, including astrocytes, neuroblasts, and contaminating cells, filtered_10X_gbm.csv only includes astrocytes and neuroblasts, and has been filtered of low quality cells) and metadata (meta_all_cells.csv, meta_filtered.csv).

molecule: total RNA

organism: Mus musculus

source_name: Cortical Astrocytes

extract_protocol:
Brains were extracted and dissected to isolate the portion of cortex subjected by injury (or contralateral hemisphere as control). Tissue was digested with Miltenyi's Brain Dissociation Kit and tdTomato+ cells were sorted on a BD FACS Influx sorter.
Libraries were prepared using Chromium Single Cell 3' Library and Gel Bead Kit (v2, 10X Genomics)

value: Astrocytes

tag: tissue

value: Cortex

tag: strain

tag: age

value: Adult (>2 months old)

tag: experimental condition

value: WT x Injured

tag: sorting

value: FACS (tdTomato+)


title: NB3_GW405833_C5D1_rep1_6h

value: Human-derived xenograft neuroblastoma (NB) primary cells


title: NB2_Rosiglitazone_C12D1_rep1_6h

value: Child


title: s_GFP3_1.5_positive_10

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s no -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing normalized counts

source_name: small intestine

extract_protocol:
RNA was extracted using Trizol reagent followed manufacture protocol (Invitrogen).
2ng of total RNA underwent cDNA pre-Amplification using CloneTech SMART-Seq v4 Ultra Low Input RNA Kit followed manufacture instruction with 12 cycles of PCR. Library preparation was followed by using KAPA Hyper prep kit according to instruction provided by KAPA Biosystems, cDNA input was normalized to 10 ng per sample as library input, with 8 cycles of PCR.

treatment_protocol: Lgr5-GFP high cells sorted from Lgr5-GFP mice were incubated with 1ng/ml IFNg in ENR media (EGF+Noggin+R-spondin1) for 1.5 hours.

value: Intestinal stem cells

value: small intestine

tag: treatment

value: culture with 1ng/ml IFNg for 1.5 hours


title: NB2_Retinoic acid_C11D2_rep1_6h

value: Retinoic acid


title: NB2_Control_CTR_rep4_6h

value: Control


title: NB3_GW405833_C5D2_rep1_6h


title: NB3_GW405833_C5D3_rep1_6h


title: NB3_Control_CTR_rep3_6h


title: NB2_DMSO2_DMSO2_rep2_6h

value: DMSO


title: NB3_JQ1_C6D2_rep1_6h


title: s_GFP3_1.5_negative_9

value: no treatment


title: s_GFP1_1.5_positive_6


title: s_GFP3_1.5_positive_2


title: healthy_wt_10X_18_015

description:
WT astrocytes
10X_18_015

value: WT x healthy


title: s_GFP3_1.5_negative_1


title: NB3_JQ1_C6D3_rep1_6h


title: s_GFP1_1.5_negative_5


title: NB3_Lovastatin_C7D1_rep1_6h

value: Lovastatin


title: NB3_JQ1_C6D1_rep1_6h


title: NB2_Rosiglitazone_C12D2_rep1_6h

value: Rosiglitazone


title: NB3_Lovastatin_C7D2_rep1_6h


title: NB3_Omiplasib_C8D2_rep1_6h

value: Omiplasib


title: NB2_PK11195_C10D3_rep1_6h


title: NB2_Retinoic acid_C11D3_rep1_6h


title: NB3_Lovastatin_C7D3_rep1_6h


title: NB2_DMSO1_DMSO1_rep2_6h


title: R36

city: Pamplona

first: Fermin

middle: I

last: Milagro

state: Navarra

address: c/ Irunlarrea 1

department: Centre for Nutrition Research

country: Spain

institute: University of Navarra

description: small RNA

data_processing:
Adapter and quality trimming using Trimmomatic with a minimun read length of 16
Alignment usign Bowtie1 and hg19 as reference
miRNA quantification using Cuffdiff and miRBase v21
Data normalization using quantiles
Genome_build: UCSC hg19
Supplementary_files_format_and_content: xlsx file includes the normalized abundance measurements of each miRNA in each sample

source_name: White blood cells

growth_protocol: White cells (buffy coat) isolated with Ficoll-Paque from blood from Caucasian obese subjects

extract_protocol:
Trizol reagent
Libraries were prepared according to Illumina's instructions.

tag: responders to diet

value: high responder


title: NB3_Omiplasib_C8D1_rep1_6h


title: NB2_Palbociclib_C9D3_rep1_6h

value: Palbociclib


title: R31

description: small RNA


title: NB2_PK11195_C10D1_rep1_6h


title: R20

description: small RNA

value: low responder


title: NB2_Palbociclib_C9D2_rep1_6h


title: NB2_Retinoic acid_C11D1_rep1_6h


title: NB2_Omiplasib_C8D3_rep1_6h


title: embryo at HH9 biological

type: RNA

city: Northridge

first: Maria Elena

last: de Bellard

state: CA

address: 18111 Nordhoff St

department: Biology

institute: California State University Northridge

description:
Gene expression data from HH9 embryos .
The library was arrayed and spotted using the Genomix Q-bot in the Genomics Technology Facility at Caltech on samples of 2 ng of DNA using 10 filters, comprising >180,000 different clones.
Total RNA extracted from each stage of purified neural crests were analyzed with Agilent micro analyzer and the integrity of total RNA by the ratio to 18s and 28s rRNA.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

label: biotin

organism: Gallus gallus

source_name: Chicken embryo isolated trunk neural crest cells

label_protocol:
The HH16-19 chick bacterial cDNA library was synthesized from embryo’s PolyA RNA using Invitrogen SuperScript cDNA Synthesis and Plasmid Cloning kit.
First strand cDNA was prepared using an oligo-dT/Not I primer/adapter and SuperScript reverse transcriptase.  Second strand cDNA was prepared using standard Gubler and Hoffman nick translational replacement of the mRNA.
SalI linkers were ligated, and the cDNA was directionally cloned into the pCMV-Sport6 vector that was included in the kit.  The library has a complexity of 1.5x108 clones/µg with an average insert size of 2kb.

extract_protocol:
Purified neural crest cells were in Ambion RNA lysis buffer and Total RNA was isolated using the Ambion RNAqueous kit. RNA samples were analyzed on a MOPS gel and spectrophotometer to determine their integrity and quantity.
Total RNA was extracted using Qiagen Kit and RNA integrity was determined with Angialent microanalizer. Total RNA macroarray analysis was done with Affymetrix gallus genome oligonucleotide and profiled by an Analysis Expression Company.

value: isolated cells from HNK1 sorting

tag: genotype

value: white leghorn chicken

value: embryos stage HH9


title: R26

description: small RNA


title: C48

description: small RNA


title: NB2_Lovastatin_C7D3_rep1_6h

value: Human-derived xenograft neuroblastoma (NB) primary cells

value: Child


title: embryo at HH19 biological

description:
Gene expression data from HH16 embryos .
The library was arrayed and spotted using the Genomix Q-bot in the Genomics Technology Facility at Caltech on samples of 2 ng of DNA using 10 filters, comprising >180,000 different clones.
Total RNA extracted from each stage of purified neural crests were analyzed with Agilent micro analyzer and the integrity of total RNA by the ratio to 18s and 28s rRNA.

value: embryos stage HH16


title: NB2_Omiplasib_C8D1_rep1_6h


title: NB2_Palbociclib_C9D1_rep1_6h


title: R03

description: small RNA


title: NB2_Omiplasib_C8D2_rep1_6h


title: embryo at HH16 biological

value: embryos stage HH19


title: NB3_Control_CTR_rep2_6h

value: Control


title: NB3_DMSO2_DMSO2_rep4_6h

value: DMSO


title: NB2_Control_CTR_rep3_6h


title: C38

description: small RNA


title: NB2_PK11195_C10D2_rep1_6h


title: C31

description: small RNA


title: NB3_Palbociclib_C9D3_rep1_6h


title: NB3_Palbociclib_C9D1_rep1_6h


title: NB3_Palbociclib_C9D2_rep1_6h


title: NB3_PK11195_C10D1_rep1_6h


title: C26

description: small RNA


title: NB3_Omiplasib_C8D3_rep1_6h


title: C16

description: small RNA


title: C06

description: small RNA


title: NB3_Retinoic acid_C11D1_rep1_6h

value: Retinoic acid


title: NB3_PK11195_C10D3_rep1_6h


title: NB3_Retinoic acid_C11D2_rep1_6h


title: NB3_DMSO1_DMSO1_rep3_6h


title: NB2_DMSO2_DMSO2_rep1_6h


title: NB2_JQ1_C6D3_rep1_6h


title: NB2_Lovastatin_C7D2_rep1_6h


title: NB2_Lovastatin_C7D1_rep1_6h


title: NB3_Retinoic acid_C11D3_rep1_6h


title: NB2_JQ1_C6D2_rep1_6h


title: NB2_JQ1_C6D1_rep1_6h


title: NB2_GW405833_C5D1_rep1_6h


title: NB2_GW405833_C5D3_rep1_6h


title: NB3_PK11195_C10D2_rep1_6h


title: NB2_GW405833_C5D2_rep1_6h


title: NB2_Control_CTR_rep2_6h


title: NB2_Fasudil_C4D2_rep1_6h

value: Fasudil


title: NB3_Rosiglitazone_C12D3_rep1_6h


title: Alpha_RNA-seq_rep1

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: total RNA minus rRNA

data_processing:
Sequencing reads were mapped to the human hg19 reference genome assembly using TopHat2 (Kim et al., 2013) with default and “--min-anchor 5” parameters. Mapped reads from multiple sequencing lanes were merged using samtools (Li et al 2009). Gene expression based on GENCODE v19 annotations (Harrow et al., 2012) was determined using HTSeq (Anders et al. 2015) on “union” mode.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing Htseq output for each sample

source_name: Primary human adult islets

growth_protocol:
Undifferentiated stem cells were maintained as aggregates in supplemented mTeSR1 medium (StemCell Technologies) using spinner flasks (Corning) set at a 70rpm rotation rate in a 37ºC 5% CO2 incubator. Directed hPSC differentiation into islet cells was conducted as described in the methods of (Alvarez-Dominguez et al. 2019).
Primary islets were cultured in supplemented CRML-1066 medium +10% FBS in low-attachment plates (Corning).

extract_protocol:
Total RNA was isolated using the miRNeasy kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was depleted from total RNA using the Ribo-Zero Gold Kit (Epicentre, Madison, WI).
Directional cDNA libraries were prepared using a KAPA Biosystems Stranded RNA-seq Library Preparation kit, pooled, and sequenced on an Illumina HiSeq 2500 platform across multiple lanes.

value: Primary human adult islets

value: Alpha Primary adult alpha cell


title: NB3_Rosiglitazone_C12D1_rep1_6h

value: Rosiglitazone


title: PH_RNA-seq_rep1

description: total RNA minus rRNA

source_name: HUES 8 hESC line

tag: cell line

value: HUES 8 hESC line

tag: protocol

value: in vitro differentiated pluripotent stem cell

tag: Stage

value: Stage 6 day 20

value: PH hPSC-derived poly-hormonal cell


title: NB3_Torin 2_C13D1_rep1_6h

value: Torin 2


title: NB3_Control_CTR_rep1_6h


title: NB3_Torin 2_C13D2_rep1_6h


title: NB3_DMSO1_DMSO1_rep2_6h


title: NB2_Fasudil_C4D3_rep1_6h


title: Beta_RNA-seq_rep1

description: total RNA minus rRNA

value: Beta Primary adult beta cell


title: NB3_DMSO2_DMSO2_rep1_6h

value: Human-derived xenograft neuroblastoma (NB) primary cells


title: PP1_RNA-seq_rep1

description: total RNA minus rRNA

value: Stage 3 day 2

value: PP1 hPSC-derived pancreatic progenitor 1


title: NB3_DMSO2_DMSO2_rep2_6h

value: Child


title: NB3_DMSO2_DMSO2_rep3_6h


title: SCbeta_RNA-seq_rep1

description: total RNA minus rRNA

value: Scbeta hPSC-derived beta cell


title: DE_RNA-seq_rep1

description: total RNA minus rRNA

value: Stage 1 day 3

value: DE hPSC-derived definitive endoderm


title: NB3_Torin 2_C13D3_rep1_6h


title: PP2_RNA-seq_rep1

description: total RNA minus rRNA

value: Stage 4 day 5

value: PP2 hPSC-derived pancreatic progenitor 2


title: NB3_DMSO1_DMSO1_rep1_6h

value: DMSO


title: NB3_Rosiglitazone_C12D2_rep1_6h

value: Rosiglitazone


title: NB2_AZDS438_C2D3_rep1_6h


title: NB2_DL-PDMP_C3D1_rep1_6h

value: DL-PDMP


title: NB2_Fasudil_C4D1_rep1_6h

value: Fasudil


title: Chromera_mixotropic

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

country: Australia

institute: CSIRO

data_processing:
Sequencing reads were quality fitered and trimmed using Trimmomatic. Processed reads were assembled using trinity software using default parameter suitable for paired-end data and min contig length of 500.  The transcriptome was annotated using the BLAST2GO suite and KEGG databases
Genome_build: denovo transcriptome
Supplementary_files_format_and_content: Trinity.genes_longest_isoform_annot: transcriptome annotation based on the longest isoform data
Supplementary_files_format_and_content: Trinity.fasta: de novo transcriptome generated by the trinity software
Supplementary_files_format_and_content: Trinity.genes_longest_isoform.fasta: transcriptome that contains the longest isoform per gene used for generation annotation

organism: Chromera velia

source_name: Algal culture

growth_protocol: Cultures were maintained at 25 °C in Guillard’s f/2 medium on 12 h/12 h day and night regime

extract_protocol:
50 mL of Chromera cultures were pelleted by spinning the cultures at 3,000 x g for 5 min. Pellets were suspended in 1 ml 0.2 μm sterile FSW and centrifuged at 3,000 x g for 5 min. Pellets were snap frozen in liquid nitrogen and stored at -80°C until further treatment. Total RNA was isolated from ~80 mg of the frozen Chromera pellets using the RNAqueous® Total RNA Isolation Kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Culture conditions included control, dark stress, cold shock, heat shock, motile and mixotrophic

value: GBR

value: Algal culture


title: NB2_DL-PDMP_C3D3_rep1_6h


title: NB2_AZDS438_C2D2_rep1_6h


title: NB2_DMSO1_DMSO1_rep1_6h


title: hPSC_RNA-seq_rep1

description: total RNA minus rRNA

value: HUES 8 hESC line

value: in vitro differentiated pluripotent stem cell

value: Stage 0

value: hPSC human pluripotent stem cell


title: EN_RNA-seq_rep1

description: total RNA minus rRNA

value: Stage 5 day 3

value: EN hPSC-derived endocrine progenitor


title: Chromera_motile


title: NB2_AS601245_C1D3_rep1_6h

value: Human-derived xenograft neuroblastoma (NB) primary cells

value: Child


title: NB2_AS601245_C1D1_rep1_6h


title: NB2_Control_CTR_rep1_6h

value: Control


title: NB2_DL-PDMP_C3D2_rep1_6h


title: Chromera_heat-shock


title: Chromera_control


title: NB2_AS601245_C1D2_rep1_6h


title: injured_hom_2_10X_18_046

description:
Rbpj-k-depleted astrocytes in SWI
10X_18_046

value: Astrocytes

value: Cortex

value: Adult (>2 months old)

value: Rbpj-K-/- x Injured

value: FACS (tdTomato+)


title: injured_hom_1_10X_18_020

description:
Rbpj-k-depleted astrocytes in SWI
10X_18_020


title: healthy_hom_10X_18_018

description:
Rbpj-k-depleted astrocytes
10X_18_018

value: Rbpj-K-/- x Healthy


title: HEPM rep3 [ATAC-seq]

city: Iowa City

first: Robert

last: Cornell

state: Iowa

address: 1-400 D Bowen Science Bldg. 51 Newton Road

department: Anatomy and Cell Biology

institute: University of Iowa

data_processing:
Sequencing reads were trimmed with Trimmomatic (0.38) using NexteraPE sequences.
Trimmed paired reads were mapped with Bowtie2 (default parameters). Sorting, removal of PCR duplicates and conversion from SAM to BAM files were performed using SAMtools
We employed DeepTools (v 2.0) to check the reproducibility of the biological replicates and generate bigWig coverage files for visualization
Peaks were called using MACS2 (v2.1.1) (parameter: --nomodel --nolambda --gsize 2.7e9 --keep-dup all --slocal 10000 ).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig and peaks bed

source_name: Human embryonic palatal mesenchymal cells

extract_protocol:
Isolated cells were lysed with 50 µL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40; all components purchased from Sigma) in a centrifuge at 500 x g for 15 minutes at 4°C.
Pelleted nuclei were resuspended in 50 µL tagmentation reaction mix (25 µL Nextera TD Buffer, 2.5 µL Nextera TD Enzyme, and 22.5 µL H2O, all from the Nextera DNA Sample Preparation Kit (Illumina). Immediately after Tn5 tagmentation, DNA samples were purified and indexed using NEBNext® High-Fidelity 2x PCR Master Mix (New England Biolabs) with a customized Nextera PCR primer pair, according to the following program: 72°C for 5 minutes; 98°C for 30 seconds; 11 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute; and hold at 4°C. All DNA libraries that exhibited a nucleosome pattern in the BioAnalyzer 2100 Assay passed the pre-sequencing QC process and were pooled for high-throughput sequencing.

treatment_protocol: For each biological replicate, 20000 HIOEC or HEPM cells were harvested for ATAC-seq library preparation.

tag: passage

value: Passage 3 after thaw

value: mesenchyme


title: HEPM rep1 [ATAC-seq]


title: PBMCs of Tharparkar cattle under heat stress at day 0, rep2

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

country: India

institute: ICAR-NBAGR

description: Gene expression in PBMCs

data_processing:
Initially, the quality-filtered reads from control and infected samples (0 days and 7 days post treatment) were mapped to bovine genome using Bowtie2. The mapped reads were then assembled using RNA-Seq by expectation maximization (RSEM).
Supplementary_files_format_and_content: TPMs, FPKMs

organism: Bos taurus

extract_protocol:
Total RNA from each subset of PBMCs of control and heat stressed cattle were isolated using the RNeasy Mini kit (Qiagen GmbH, Germany). The integrity and quantity of isolated RNA were assessed  based on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples were found greater than 8, which is considered suitable for further processing. protocol.
Library was prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NewEngland Biolabs Inc.) following the manufacturer’s protocol. Approximately, 100ng of RNA from each sample was used for RNA library preparation. The quality of the libraries was assessed on Bioanalyzer and further quantified using a Qubit 2.0 Fluorometer (Life technologies) and by qPCR. Libraries were sequenced on Illumina – NextSeq500  following manufacturer’s protocol.

treatment_protocol: Tharparkar and Crossbred were subjected to heat for a period of 7 day  and PBMCs were isolated from them. RNA was  isolated from PBMCs of both genetic groups  before ( 0 days )  and post heat stress (7 day )  .

tag: breed

value: Tharparkar

tag: stress

value: heat stress

tag: time

value: 0 day

tag: cell type

value: PBMC


title: NB2_AZDS438_C2D1_rep1_6h

tag: passages

tag: cell line id

tag: chemical compound

tag: time point


title: BMDMs, BCG stimulated

city: Fort Collins

first: Angelo

last: Izzo

state: Colorado

address: 1682 Campus Delivery

department: MIcrobiology, Immunology, and Pathology

institute: Colorado State University

description: test

data_processing:
Data were analyzed using the Qiagen online Data Analysis Center.
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, GAPDH, ACTB, GUSB, HSP90AB1
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
In the Fold Change Template the data is fold change in cytokine expression for BMDM cells stimulated with BCG versus BMDM stimulated with gamma-irradiated BCG compated to unstimulated cells

label: Sybr Green

source_name: bone marrow derived macrophages

label_protocol: RNA was then converted into cDNA using an iScript cDNA synthesis kit (BioRad, Hercules, CA), and RT-PCR was performed using the Qiagen RT2 ProfilerTM PCR Array for Mouse Cytokines and Chemokines on a CFX ConnectTM Real-Time PCR Detection System (BioRad).

growth_protocol: Bone marrow cells were harvested from C57BL/6 mice and added to complete RPMI containing 20 ng/mL M-CSF (macrophage colony-stimulating factor; Peprotech, Rocky Hill, NJ) to drive macrophage differentiation.  Media was changed every 72 hours until the eighth day in which media was changed to exclude M-CSF and antibiotics.  On day seven, cells were harvested and brought to a concentration of 1.0x106 macrophages per well in a 24 well plate for stimulation for 24 and 48 hours with varying MOI of BCG or irrBCG.  Supernatants and total RNA was harvested at each time point.

extract_protocol: Total RNA was isolated using TRIZol® (Invitrogen), and quantified using a Nanodrop Microvolume Spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: BCG or irrBCG for 24 hours compared to unstimulated cells

value: macrophage

tag: strain

value: BCG

value: 24 hours


title: HIOEC day 3 rep2 [ATAC-seq]

source_name: Immortalized human oral epithelial cell line

tag: tissue

value: epithelium


title: BMDMs, irrBCG stimulated

description: test

tag: treatment

value: gamma-irradiated BCG


title: Chromera_cold-shock

value: GBR

value: Algal culture


title: Chromera_dark


title: PBMCs of Crossbred cattle under heat stress at day 7, rep2

description: Gene expression in PBMCs

value: Crossbred

value: 7 days


title: PBMCs of Tharparkar cattle under heat stress at day 7, rep2

description: Gene expression in PBMCs


title: BMDMs, Unstimulated

description: control

value: control


title: HEPM rep2 [ATAC-seq]


title: HIOEC day 3 rep3

data_processing:
Sequencing reads were trimmed with Trimmomatic (0.38) using TrueSeq3PE sequences.
Trimmed paired reads were mapped with Bowtie2 (default parameters). Sorting, removal of PCR duplicates and conversion from SAM to BAM files were performed using SAMtools
We employed DeepTools (v 2.0) to check the reproducibility of the biological replicates and generate bigWig coverage files for visualization
Peaks were called using MACS2 (v2.1.1) (parameter: --nomodel --nolambda --gsize 2.7e9 --keep-dup all --slocal 10000 ).
Genome_build: hg19
Supplementary_files_format_and_content: bw, peaks bed

extract_protocol:
Cell were washed with ice-cold PBS (Hyclone) and fixed with 1% paraformaldehyde (PFA) for 10min at room temperature. PFA was then quenched in 134M Glycine (Sigma) for 5 min at room temperature, and cells were collected with a cell scraper in ice-cold PBS. After centrifuge for 10 mins at 500g, the cell pellets were resuspended with 5mM PIPES pH8.5, 85mM KCl, 1% (v/v) IGEPAL CA-630, 50mM NaF, 1mM PMSF, 1mM phenylarsine oxide, 5mM Sodium Orthovanadate and protease inhibitor cocktail (Roche, Germany). After sonication, chromatin immunoprecipitation was performed using 4ug of anti-Histone H3, Acetylated Lysine 27 (H3K27Ac) (Abcam, Cambridge, UK, ab4729)  per 500,000 cells.
ChIP-seq library were indexed with kit (ND606-01, Vanzyme, China)

treatment_protocol: For each biological replicate, 500000 HIOEC cells were harvested for ATAC-seq library preparation.

tag: antibody


title: PBMCs of Tharparkar cattle under heat stress at day 0, rep1

description: Gene expression in PBMCs


title: PBMCs of Tharparkar cattle under heat stress at day 7, rep1

description: Gene expression in PBMCs


title: HIOEC day 3 rep3 [ATAC-seq]


title: PBMCs of Crossbred cattle under heat stress at day 0, rep2

description: Gene expression in PBMCs


title: PBMCs of Crossbred cattle under heat stress at day 0, rep1

description: Gene expression in PBMCs


title: HIOEC day 3 rep2


title: PBMCs of Crossbred cattle under heat stress at day 7, rep1

description: Gene expression in PBMCs


title: Pca4: The paracancer in case 4

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

country: China

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Expression data from rectal paracancer epithelial cells of case 4

hyb_protocol: Following labeling, cDNA was hybridized on a Clariom  D Array(human, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console installed in the GeneChip Scanner 3000 7G.

data_processing: The data was analyzed with the Robust Multichip Analysis (RMA) algorithm, using the Affymetrix default analysis settings.

source_name: Paracancer tissue of human rectal cancer in case 4

label_protocol: Biotinylated cDNA was prepared from 250 ng total RNA according to the manufacturer’s standard protocol (Affymetrix).

growth_protocol: Rectal cancer tissues and matched adjacent non-cancerous tissues were immediately stored in liquid nitrogen or stored in the -80 ℃ refrigerator after 2 hours.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Each time about 100mg of tissue samples were placed into 1.5ml EP tubes containing Trizol lysate and the tissue samples were ground on ice with a tissue grinder.

value: Paracancer epithelium of human rectal cancer


title: Pca5: The paracancer in case 5

description: Expression data from rectal paracancer epithelial cells of case 5

source_name: Paracancer tissue of human rectal cancer in case 5


title: HIOEC day 3 rep1

value: Passage 3 after thaw


title: Pca6: The paracancer in case 6

description: Expression data from rectal paracancer epithelial cells of case 6

source_name: Paracancer tissue of human rectal cancer in case 6


title: Pca1: The paracancer in case 1

description: Expression data from rectal paracancer epithelial cells of case 1

source_name: Paracancer tissue of human rectal cancer in case 1


title: Pca2: The paracancer in case 2

description: Expression data from rectal paracancer epithelial cells of case 2

source_name: Paracancer tissue of human rectal cancer in case 2


title: HIOEC day 3 rep1 [ATAC-seq]


title: Ca5: The cancerous tissue of case 5

description: Expression data from rectal cancer cells of case 5

source_name: Human rectal cancer tissue in case 5

value: Human rectal cancer tissue


title: Pca3: The paracancer in case 3

description: Expression data from rectal paracancer epithelial cells of case 3

source_name: Paracancer tissue of human rectal cancer in case 3


title: Ca2: The cancerous tissue of case 2

description: Expression data from rectal cancer cells of case 2

source_name: Human rectal cancer tissue in case 2


title: EAE107 Co dist A1-1

status: Public on Nov 01 2019

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

country: Germany

institute: Institute of Clinical Molecular Biology

description:
colonic tissue from mouse under Tryptophan-proficient diet
H01593

data_processing:
Sequence reads from were trimmed for adapters using the software Trimgalore (version 0.4.4)
All filtered reads were mapped to the GRCm38 reference using the software STAR (version 2.5.2b)
Expression counts of genes were estimated using featureCounts (version 1.5.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files with expression counts for each sample

source_name: distal colon tissue

extract_protocol:
Total RNA was extracted from frozen colon whole tissues of the mice using the RNeasy mini kit from Qiagen using standard protocol. The frozen tissue samples were homogenized using Tissue Lyser II for the RNA extraction.
Individual strand-specific single-end sequencing libraries were constructed from the total RNA isolated from the samples using TruSeq Stranded mRNA kit (Illumina Inc.). Sequencing was performed on the Illumina HiSeq3000 (1 x 50 bp) using standard protocols.

value: distal colon tissue

tag: condition

value: Trp-prof

tag: gender

value: female


title: EAE107 Co dist A1-0

description:
colonic tissue from mouse under Tryptophan-proficient diet
H01592


title: EAE107 Co dist A2-3

description:
colonic tissue from mouse under Tryptophan-proficient diet
H01590


title: EAE107 Co dist A1-3

description:
colonic tissue from mouse under Tryptophan-proficient diet
H01595


title: EAE107 Co dist A2-4

description:
colonic tissue from mouse under Tryptophan-proficient diet
H01591


title: EAE107 Co dist A1-2

description:
colonic tissue from mouse under Tryptophan-proficient diet
H01594


title: Ca6: The cancerous tissue of case 6

description: Expression data from rectal cancer cells of case 6

source_name: Human rectal cancer tissue in case 6


title: EAE107 Co dist A2-2

description:
colonic tissue from mouse under Tryptophan-proficient diet
H01589


title: EAE107 Co dist B1-3

description:
colonic tissue from mouse under Tryptophan-deficient diet
H01585

value: Trp-def


title: EAE107 Co dist B1-4

description:
colonic tissue from mouse under Tryptophan-deficient diet
H01586


title: EAE107 Co dist A2-0

description:
colonic tissue from mouse under Tryptophan-proficient diet
H01587


title: EAE107 Co dist B1-2

description:
colonic tissue from mouse under Tryptophan-deficient diet
H01584


title: Ca3: The cancerous tissue of case 3

description: Expression data from rectal cancer cells of case 3

source_name: Human rectal cancer tissue in case 3


title: EAE107 Co dist B1-1

description:
colonic tissue from mouse under Tryptophan-deficient diet
H01583


title: EAE107 Co dist A1-4

description:
colonic tissue from mouse under Tryptophan-proficient diet
H01596


title: EAE107 Co dist B1-0

description:
colonic tissue from mouse under Tryptophan-deficient diet
H01582


title: Ca1: The cancerous tissue of case 1

description: Expression data from rectal cancer cells of case 1

source_name: Human rectal cancer tissue in case 1


title: EAE107 Co dist B2-3

description:
colonic tissue from mouse under Tryptophan-deficient diet
H01580


title: EAE107 Co dist B2-1

description:
colonic tissue from mouse under Tryptophan-deficient diet
H01578


title: EAE107 Co dist B2-0

description:
colonic tissue from mouse under Tryptophan-deficient diet
H01577


title: TFEBwt5_CCR2pos_CX3CR1-Cre

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
Illumina Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the mRNA transcriptome, defined by a gtf for the GRCm38 genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the gtf file.
The data have not been further normalized or manipulated, so that each user can perform sample (library) depth and other normalization using software such as DESeq or edgeR.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes htseq-count values for each mRNA that was present at >= 0.5 reads per million in any sample (12795 mRNAs).

growth_protocol: Cx3cr1-er-Cre TFEB-LoxP-STOP Td-Tomato-LoxSTOP versus controls (Cx3cr1-er-Cre Td-Tomato-LoxSTOP)

extract_protocol:
Qiagen
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 1-50ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using duty cycle 10, intensity 5, cycles/burst 200, time 180 seconds. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.
non-strand-specific, single-end RNA-Seq

treatment_protocol: After instrumentation, mice were fed tamoxifen to induce TFEB. After 7 days induction, mice underwent ischemia for 90 minutes. 7 days after ischemic injury, mice underwent flow sorting for cardiac macrophages. CCR2+ TFEB and CCR2- TFEB macrophages were compared to control CCR2+ and CCR2- macrophages from post-IR hearts.

tag: genotype

value: Flow-sorted cardiac macrophage


title: TFEBwt5_CCR2pos_Cre-neg


title: TFEBwt5_CCR2neg_CX3CR1-Cre


title: TFEBwt5_CCR2neg_Cre-neg


title: TFEBwt4_CCR2pos_CX3CR1-Cre


title: TFEBwt4_CCR2neg_Cre-neg


title: EAE107 Co dist B2-2

description:
colonic tissue from mouse under Tryptophan-deficient diet
H01579


title: TFEBwt4_CCR2neg_CX3CR1-Cre


title: TFEBwt4_CCR2pos_Cre-neg


title: TFEBwt3_CCR2pos_Cre-neg


title: TFEBwt3_CCR2pos_CX3CR1-Cre


title: TFEBwt2_CCR2pos_CX3CR1-Cre


title: TFEBwt3_CCR2neg_Cre-neg


title: Ca4: The cancerous tissue of case 4

description: Expression data from rectal cancer cells of case 4

source_name: Human rectal cancer tissue in case 4


title: TFEBwt2_CCR2neg_CX3CR1-Cre


title: Control ChIP-seq from suprapubic skin (ENCLB076FAW)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR531AUV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR531AUV
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB076FAW
size range: 200-600

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens male adult (37 years) suprapubic skin tissue

value: Control

value: suprapubic skin

value: tissue

tag: description

value: EnTEX:Skin - Not Sun Exposed (Suprapubic) updated Feb 2019 with updated term name and ID from DCC.

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 37 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS874KYB at ENCODE; https://www.encodeproject.org/ENCBS874KYB/


title: TFEBwt2_CCR2pos_Cre-neg

tag: cell type


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB500SYL)

description:
https://www.encodeproject.org/experiments/ENCSR525JJM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR525JJM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR147KFH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB500SYL
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS884JOD at ENCODE; https://www.encodeproject.org/ENCBS884JOD/


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB203LMZ)

description:
https://www.encodeproject.org/experiments/ENCSR522MTS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR522MTS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR147KFH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB203LMZ
fragmentation methods: sonication (generic)
size range: 200-600


title: Control ChIP-seq from stomach (ENCLB405BYI)

description:
https://www.encodeproject.org/experiments/ENCSR538MSN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR538MSN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB405BYI
size range: 200-600

source_name: Homo sapiens male adult (37 years) stomach tissue

value: stomach

value: ENCBS940XKF at ENCODE; https://www.encodeproject.org/ENCBS940XKF/


title: Histone ChIP-seq from stomach (ENCLB627PPJ)

description:
https://www.encodeproject.org/experiments/ENCSR552ICY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR552ICY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR538MSN
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB627PPJ
fragmentation methods: sonication (generic)
size range: 200-600


title: TFEBwt3_CCR2neg_CX3CR1-Cre

value: Flow-sorted cardiac macrophage


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB932JRY)

description:
https://www.encodeproject.org/experiments/ENCSR525JJM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR525JJM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR147KFH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB932JRY
fragmentation methods: sonication (generic)
size range: 200-600


title: Control ChIP-seq from stomach (ENCLB656KMT)

description:
https://www.encodeproject.org/experiments/ENCSR538MSN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR538MSN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB656KMT
size range: 200-600

value: Control


title: TFEBwt1_CCR2pos_CX3CR1-Cre


title: TFEBwt2_CCR2neg_Cre-neg


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB151XUT)

description:
https://www.encodeproject.org/experiments/ENCSR522MTS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR522MTS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR147KFH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB151XUT
fragmentation methods: sonication (generic)
size range: 200-600


title: Control ChIP-seq from suprapubic skin (ENCLB288HSQ)

description:
https://www.encodeproject.org/experiments/ENCSR531AUV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR531AUV
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB288HSQ
size range: 200-600

value: suprapubic skin


title: Histone ChIP-seq from stomach (ENCLB818GZW)

description:
https://www.encodeproject.org/experiments/ENCSR552ICY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR552ICY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR538MSN
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB818GZW
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: TFEBwt1_CCR2pos_Cre-neg


title: Histone ChIP-seq from tibial nerve (ENCLB223GFA)

description:
https://www.encodeproject.org/experiments/ENCSR981CTV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR981CTV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB223GFA
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) tibial nerve tissue

extract_protocol: not provided

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: ENCBS647STW at ENCODE; https://www.encodeproject.org/ENCBS647STW/


title: Histone ChIP-seq from tibial nerve (ENCLB705RIA)

description:
https://www.encodeproject.org/experiments/ENCSR981CTV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR981CTV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB705RIA
fragmentation methods: sonication (generic)
size range: 200-600

value: male

value: adult

value: 37 year


title: Histone ChIP-seq from tibial nerve (ENCLB344PWT)

description:
https://www.encodeproject.org/experiments/ENCSR516LQO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR516LQO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB344PWT
fragmentation methods: sonication (generic)
size range: 200-600

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: TFEBTG4_CCR2pos_Cre-neg


title: TFEBTG4_CCR2pos_mac-TFEB


title: TFEBwt1_CCR2neg_Cre-neg


title: TFEBTG4_CCR2neg_mac-TFEB


title: Histone ChIP-seq from tibial nerve (ENCLB321BLE)

description:
https://www.encodeproject.org/experiments/ENCSR516LQO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR516LQO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB321BLE
fragmentation methods: sonication (generic)
size range: 200-600


title: Histone ChIP-seq from spleen (ENCLB193LRI)

description:
https://www.encodeproject.org/experiments/ENCSR506DCR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR506DCR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB193LRI
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) spleen tissue

value: spleen

value: ENCBS486GAC at ENCODE; https://www.encodeproject.org/ENCBS486GAC/


title: Histone ChIP-seq from spleen (ENCLB530SAC)

description:
https://www.encodeproject.org/experiments/ENCSR506DCR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR506DCR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB530SAC
fragmentation methods: sonication (generic)
size range: 200-600


title: Control ChIP-seq from breast epithelium (ENCLB295PQR)

description:
https://www.encodeproject.org/experiments/ENCSR980TBV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR980TBV
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB295PQR
size range: 200-600

source_name: Homo sapiens female adult (51 year) breast epithelium tissue

value: breast epithelium

value: EnTEX:Breast - Mammary Tissue updated Feb 2019 with updated term name and ID from DCC.

value: female

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS444JDU at ENCODE; https://www.encodeproject.org/ENCBS444JDU/


title: TFEBTG4_CCR2neg_Cre-neg

value: Flow-sorted cardiac macrophage


title: Control ChIP-seq from breast epithelium (ENCLB669NJI)

description:
https://www.encodeproject.org/experiments/ENCSR980TBV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR980TBV
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB669NJI
size range: 200-600

value: Control

value: tissue


title: TFEBTG2_CCR2neg_Cre-neg


title: TFEBTG3_CCR2pos_Cre-neg


title: TFEBTG3_CCR2neg_mac-TFEB


title: Histone ChIP-seq from tibial artery (ENCLB216HOK)

description:
https://www.encodeproject.org/experiments/ENCSR960VRR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR960VRR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB216HOK
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens male adult (37 years) tibial artery tissue

value: tibial artery

value: EnTEX:Artery - Tibial

value: male

value: ENCBS452GMG at ENCODE; https://www.encodeproject.org/ENCBS452GMG/


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB676HWP)

description:
https://www.encodeproject.org/experiments/ENCSR965BLU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR965BLU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR343GIV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB676HWP
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) gastroesophageal sphincter tissue

value: gastroesophageal sphincter

value: EnTEX:Esophagus - Gastroesophageal Junction updated Feb 2019 with updated term name and ID from DCC.

value: adult

value: 37 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS727XQL at ENCODE; https://www.encodeproject.org/ENCBS727XQL/


title: TFEBTG3_CCR2pos_mac-TFEB


title: TFEBTG2_CCR2neg_mac-TFEB


title: Histone ChIP-seq from tibial nerve (ENCLB490FPB)

description:
https://www.encodeproject.org/experiments/ENCSR516LQO/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR516LQO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB490FPB
fragmentation methods: sonication (generic)
size range: 200-600

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS647STW at ENCODE; https://www.encodeproject.org/ENCBS647STW/


title: Histone ChIP-seq from tibial artery (ENCLB471ATS)

description:
https://www.encodeproject.org/experiments/ENCSR960VRR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR960VRR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB471ATS
fragmentation methods: none
size range: 200-600


title: Histone ChIP-seq from sigmoid colon (ENCLB089JCV)

description:
https://www.encodeproject.org/experiments/ENCSR960AAL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR960AAL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099RQB
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB089JCV
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) sigmoid colon tissue

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: ENCBS365ZJJ at ENCODE; https://www.encodeproject.org/ENCBS365ZJJ/


title: TFEBTG1_CCR2pos_mac-TFEB

value: Flow-sorted cardiac macrophage


title: TFEBTG2_CCR2pos_mac-TFEB


title: TFEBwt1_CCR2neg_CX3CR1-Cre


title: TFEBTG3_CCR2neg_Cre-neg


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB853OBX)

description:
https://www.encodeproject.org/experiments/ENCSR965BLU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR965BLU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR343GIV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB853OBX
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: male


title: TFEBTG2_CCR2pos_Cre-neg


title: Histone ChIP-seq from sigmoid colon (ENCLB395NFO)

description:
https://www.encodeproject.org/experiments/ENCSR960AAL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR960AAL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099RQB
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB395NFO
fragmentation methods: sonication (generic)
size range: 200-600


title: TFEBTG1_CCR2pos_Cre-neg


title: Histone ChIP-seq from right atrium auricular region (ENCLB420LDE)

description:
https://www.encodeproject.org/experiments/ENCSR954TSY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR954TSY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB420LDE
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) right atrium auricular region tissue

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

value: female

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS088JMY at ENCODE; https://www.encodeproject.org/ENCBS088JMY/


title: TFEBTG1_CCR2neg_mac-TFEB


title: TFEBTG1_CCR2neg_Cre-neg


title: Histone ChIP-seq from upper lobe of left lung (ENCLB068TJN)

description:
https://www.encodeproject.org/experiments/ENCSR505YFA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR505YFA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR746QZL
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB068TJN
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: adult

value: 37 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS943JOF at ENCODE; https://www.encodeproject.org/ENCBS943JOF/


title: Histone ChIP-seq from right atrium auricular region (ENCLB173HCM)

description:
https://www.encodeproject.org/experiments/ENCSR954TSY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR954TSY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB173HCM
fragmentation methods: none
size range: 200-600


title: Histone ChIP-seq from upper lobe of left lung (ENCLB896PTB)

description:
https://www.encodeproject.org/experiments/ENCSR505YFA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR505YFA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR746QZL
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB896PTB
fragmentation methods: sonication (generic)
size range: 200-600

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Histone ChIP-seq from stomach (ENCLB307SVQ)

description:
https://www.encodeproject.org/experiments/ENCSR503XFW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR503XFW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR538MSN
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB307SVQ
fragmentation methods: sonication (generic)
size range: 200-600

value: stomach

value: ENCBS940XKF at ENCODE; https://www.encodeproject.org/ENCBS940XKF/


title: Histone ChIP-seq from stomach (ENCLB818DPD)

description:
https://www.encodeproject.org/experiments/ENCSR493MQY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR493MQY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR538MSN
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB818DPD
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB777SAA)

description:
https://www.encodeproject.org/experiments/ENCSR952BJX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR952BJX
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR156WTZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB777SAA
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa updated Feb 2019 with updated term name and ID from DCC.

value: male

value: ENCBS608MZC at ENCODE; https://www.encodeproject.org/ENCBS608MZC/


title: Histone ChIP-seq from stomach (ENCLB714COP)

description:
https://www.encodeproject.org/experiments/ENCSR493MQY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR493MQY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR538MSN
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB714COP
fragmentation methods: sonication (generic)
size range: 200-600


title: TF ChIP-seq from prostate gland (ENCLB166VBB)

description:
https://www.encodeproject.org/experiments/ENCSR946MNG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR946MNG
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB166VBB
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) prostate gland tissue

value: CTCF

value: prostate gland

value: EnTEX:Prostate updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS985DZK at ENCODE; https://www.encodeproject.org/ENCBS985DZK/


title: TF ChIP-seq from suprapubic skin (ENCLB609RFP)

description:
https://www.encodeproject.org/experiments/ENCSR485VQV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR485VQV
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB609RFP
fragmentation methods: sonication (generic)
size range: 200-600

value: suprapubic skin

value: EnTEX:Skin - Not Sun Exposed (Suprapubic) updated Feb 2019 with updated term name and ID from DCC.

value: adult

value: ENCBS874KYB at ENCODE; https://www.encodeproject.org/ENCBS874KYB/


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB062XKA)

description:
https://www.encodeproject.org/experiments/ENCSR952BJX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR952BJX
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR156WTZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB062XKA
fragmentation methods: sonication (generic)
size range: 200-600

value: 37 year

value: Bradley Bernstein, Broad


title: TF ChIP-seq from prostate gland (ENCLB793JVC)

description:
https://www.encodeproject.org/experiments/ENCSR946MNG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR946MNG
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB793JVC
fragmentation methods: sonication (generic)
size range: 200-600

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Histone ChIP-seq from upper lobe of left lung (ENCLB406YUK)

description:
https://www.encodeproject.org/experiments/ENCSR469YCE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR469YCE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR746QZL
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB406YUK
fragmentation methods: sonication (generic)
size range: 200-600

value: upper lobe of left lung

value: tissue

value: ENCBS943JOF at ENCODE; https://www.encodeproject.org/ENCBS943JOF/


title: EAE107 Co dist A2-1

description:
colonic tissue from mouse under Tryptophan-proficient diet
H01588

source_name: distal colon tissue

value: distal colon tissue

value: Trp-prof

value: female


title: TF ChIP-seq from suprapubic skin (ENCLB264YYY)

description:
https://www.encodeproject.org/experiments/ENCSR485VQV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR485VQV
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB264YYY
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: male


title: Histone ChIP-seq from upper lobe of left lung (ENCLB992YNP)

description:
https://www.encodeproject.org/experiments/ENCSR469YCE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR469YCE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR746QZL
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB992YNP
fragmentation methods: sonication (generic)
size range: 200-600


title: LNCAP_siATF4_3

city: Oslo

first: Fahri

last: Saatcioglu

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

description: replicate_3 (excluded from the analysis as this experiment is an outlier compared to the rest)

hyb_protocol: 750 ng biotin-labelled cRNA was hybridized overnight, to HumanHT-12 Expression BeadChips (Illumina Inc., CA, USA)

scan_protocol: The BeadChips were scanned with the Illumina HiScann instrument, according to the manufacturer’s instructions and data were extracted using Illumina’s BeadStudio software (gene expression module v3.0.19.0).

data_processing: The data were log2 transformed and quntile normalised using lumi R-package. Differentially expressed genes were identified using limma R package.

source_name: Prostate Cancer Cell Line

label_protocol: cRNA was prepared with Ambion's Illumina® TotalPrep™ RNA Amplification Kit (Thermo Fisher Scientific, MA, USA), using 300 ng total RNA as input material.

growth_protocol: LNCap cells were purchased from the American Type Culture Collection (Rockville, MD) and cultured in 10 % FBS containing RPMI medium.

extract_protocol: RNA was extracted using Trizol reagent according to the standart protocols.

treatment_protocol: LNCaP cells were transfected with control siRNA or an ATF4-specific siRNA, and 4 days later treated  with 300nM Tg for 5h.


title: LNCAP_siATF4_1


title: LNCAP_siATF4_2


title: MWCL_CTRL-2

city: Houston

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader.

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value. For further analysis, probes were only retained if at least 2 of the 8 samples (25%) had values above the detection threshold.

label_protocol: 300 ng of total RNA was reverse-transcribed, biotinylated, and amplified by standard Eberwine labeling with the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Cells were propagated in RPMI 1640 media supplemented with 10% fetal calf serum, 2 mM L-glutamine, 100 U/mL of penicillin, and 100 μg/mL of streptomycin.

extract_protocol: Total RNA was isolated from harvested cells with RNA mini isolation kits (Qiagen) with subsequent RNA quality assessment using an Agilent 2100 Bioanalyzer.

treatment_protocol: Cell lines BCWM.1 and MWCL-1 were treated with R191 at 1.25 uM for 24 hr, and compared to untreated cells.

tag: cell line

value: Waldenstrom’s macroglobulinemia


title: MWCL_R191-2


title: MWCL_CTRL-1


title: MWCL_R191-1


title: BWCN_CTRL-2


title: Histone ChIP-seq from stomach (ENCLB464ZTU)

description:
https://www.encodeproject.org/experiments/ENCSR944KAZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR944KAZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR538MSN
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB464ZTU
fragmentation methods: sonication (generic)
size range: 200-600

value: stomach

value: ENCBS940XKF at ENCODE; https://www.encodeproject.org/ENCBS940XKF/


title: LNCAP_siCTRL_1

value: siCTRL


title: Histone ChIP-seq from stomach (ENCLB532ZQD)

description:
https://www.encodeproject.org/experiments/ENCSR944KAZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR944KAZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR538MSN
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB532ZQD
fragmentation methods: sonication (generic)
size range: 200-600

value: adult


title: LNCAP_siCTRL_2


title: BWCN_R191-2


title: Histone ChIP-seq from right atrium auricular region (ENCLB139GML)

description:
https://www.encodeproject.org/experiments/ENCSR459CKR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR459CKR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB139GML
fragmentation methods: sonication (generic)
size range: 200-600

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS524KBT at ENCODE; https://www.encodeproject.org/ENCBS524KBT/


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB584IJI)

description:
https://www.encodeproject.org/experiments/ENCSR463NAD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR463NAD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR644XSS
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB584IJI
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: tissue

value: EnTEX:Esophagus - Mucosa

value: 54 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS143WXN at ENCODE; https://www.encodeproject.org/ENCBS143WXN/


title: BWCN_CTRL-1

value: Waldenstrom’s macroglobulinemia


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB927OTD)

description:
https://www.encodeproject.org/experiments/ENCSR463NAD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR463NAD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR644XSS
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB927OTD
fragmentation methods: sonication (generic)
size range: 200-600

value: male


title: Histone ChIP-seq from stomach (ENCLB207EMN)

description:
https://www.encodeproject.org/experiments/ENCSR503XFW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR503XFW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR538MSN
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB207EMN
fragmentation methods: sonication (generic)
size range: 200-600

value: stomach

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS940XKF at ENCODE; https://www.encodeproject.org/ENCBS940XKF/


title: LNCAP_siCTRL_3

value: siCTRL


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB129PSZ)

description:
https://www.encodeproject.org/experiments/ENCSR939CJE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR939CJE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR343GIV
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB129PSZ
fragmentation methods: sonication (generic)
size range: 200-600

value: gastroesophageal sphincter

value: EnTEX:Esophagus - Gastroesophageal Junction updated Feb 2019 with updated term name and ID from DCC.

value: adult

value: ENCBS727XQL at ENCODE; https://www.encodeproject.org/ENCBS727XQL/


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB483OSG)

description:
https://www.encodeproject.org/experiments/ENCSR939CJE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR939CJE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR343GIV
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB483OSG
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: BWCN_R191-1


title: Histone ChIP-seq from Peyer's patch (ENCLB217JOM)

description:
https://www.encodeproject.org/experiments/ENCSR440PMP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR440PMP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR708OCZ
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB217JOM
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) Peyer's patch tissue

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS388XLV at ENCODE; https://www.encodeproject.org/ENCBS388XLV/


title: Histone ChIP-seq from Peyer's patch (ENCLB967WXN)

description:
https://www.encodeproject.org/experiments/ENCSR440PMP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR440PMP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR708OCZ
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB967WXN
fragmentation methods: sonication (generic)
size range: 200-600

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: Histone ChIP-seq from breast epithelium (ENCLB182MEU)

description:
https://www.encodeproject.org/experiments/ENCSR936LAH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR936LAH
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR980TBV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB182MEU
fragmentation methods: none
size range: 200-600

value: breast epithelium

value: EnTEX:Breast - Mammary Tissue updated Feb 2019 with updated term name and ID from DCC.

value: female

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS444JDU at ENCODE; https://www.encodeproject.org/ENCBS444JDU/


title: Histone ChIP-seq from breast epithelium (ENCLB627CBU)

description:
https://www.encodeproject.org/experiments/ENCSR936LAH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR936LAH
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR980TBV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB627CBU
fragmentation methods: none
size range: 200-600


title: Input_ChIPseq_WT_liver

city: Huddinge

first: Rongrong

last: Fan

address: Hälsovägen 7c

data_processing:
ChIP-seq raw files (fastq files) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Raw tag counts files are in txt format and contain the merged peaks, annotation and raw tag counts of the respective peaks in the indicated samples. Bed files contain the genomic coordinates, tag counts, fold changes and p value of each peak.

source_name: Liver

extract_protocol:
Fresh mouse livers were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
ChIPed DNA was processed using Rubicon ThruPLEX DNA-seq kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.

treatment_protocol: All mice under normal chow diet

tag: strain

value: 8-12 week

tag: genotype/variation

value: liver

tag: chip antibody


title: Input_ChIPseq_LKO_liver

tag: tissue


title: PDMC_IBMX_24hr_rep2

city: New Taipei

first: Chih-Cheng

last: Chien

address: No 2, Ln 59, Jian-Cheng Rd, Sijhih Dist

country: Taiwan

institute: Sijhih Cathay General Hospital

description: 0.4 mM IBMX

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: PDMC, IBMX, 24hr, replicate 2

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

extract_protocol: RNeasy Mini Kit (Qiagen, Hilden, Germany) were used to extract total cellular RNA. Before microarray hybridization, each RNA sample was quantified using NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and qualified using Bioanalyzer RNA Nano 6000 chip (Agilent Technologies, Santa Clara, CA, USA).

value: placenta

tag: differentiation status

value: IBMX-induced neuronal differentiation


title: PDMC_IBMX_12hr_rep1

description: 0.4 mM IBMX

source_name: PDMC, IBMX, 12hr, replicate 1

tag: gender


title: Nucleus Oprm1-Cre:H2BG Mu_P23

first: Konstantinos

last: Meletis

address: Solnavagen 9

department: Neuroscience

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt

data_processing:
fastq files were aligned to mouse genome version mm10
 The alignments of reads towards the indicated genome assembly using SAMtools
The expression values were computed per gene as described in Ramsköld et al (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo
Clustering and marker identification was done using the Seurat package in R (versions 1.4.0 and 2.3.2)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene

source_name: Oprm1-Cre nucleus striatum

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

tag: background strain

tag: genotype

tag: treatment

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_P18


title: Nucleus Oprm1-Cre:H2BG Mu_P21


title: Nucleus Oprm1-Cre:H2BG Mu_P19


title: Nucleus Oprm1-Cre:H2BG Mu_P22


title: Nucleus Oprm1-Cre:H2BG Mu_P24


title: Nucleus Oprm1-Cre:H2BG Mu_P17


title: Histone ChIP-seq from spleen (ENCLB729GGB)

description:
https://www.encodeproject.org/experiments/ENCSR426VHO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR426VHO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB729GGB
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) spleen tissue

tag: antibody

value: spleen

value: tissue

tag: description

tag: biosample encode accession

tag: Sex

value: male

value: adult

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS486GAC at ENCODE; https://www.encodeproject.org/ENCBS486GAC/


title: PDMC_IBMX_12hr_rep2

description: 0.4 mM IBMX

source_name: PDMC, IBMX, 12hr, replicate 2

tag: age


title: Nucleus Oprm1-Cre:H2BG Mu_P20


title: Histone ChIP-seq from spleen (ENCLB361GZX)

description:
https://www.encodeproject.org/experiments/ENCSR426VHO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR426VHO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB361GZX
fragmentation methods: sonication (generic)
size range: 200-600

tag: dev stage

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link


title: Nucleus Oprm1-Cre:H2BG Mu_P15


title: Nucleus Oprm1-Cre:H2BG Mu_P16


title: PDMC_IBMX_0hr_rep1

description: 0.4 mM IBMX

source_name: PDMC, IBMX, 0hr, replicate 1

value: female

value: undifferentiated


title: PDMC_IBMX_24hr_rep1

description: 0.4 mM IBMX

source_name: PDMC, IBMX, 24hr, replicate 1


title: Nucleus Oprm1-Cre:H2BG Mu_P14


title: Tumor 10

city: Shanghai

first: Sunwang

last: Xu

address: 160 Pujian Road, Shanghai, China

institute: Renji Hospital affiliated to Shanghai Jiao Tong University School of Medicine

description: processed data file: all.rpkm.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13.
HISAT2.1.0 mapping to reference genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: all.rpkm.txt: Tab-delimited text file includes RPKM values for each Sample.

source_name: gallbladder tissue

growth_protocol: The fresh tumorous tissues and matched normal tissue were obtained from surgery.

extract_protocol:
Total RNA was extracted from tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Agilent) and kept at -80℃. The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The tissues were lysed in Trizol directly and do total RNA extraction.

tag: diagnosis

value: gallbladder cancer

value: gallbladder tumor

tag: individual


title: Tumor 9

description: processed data file: all.rpkm.txt

tag: tissue


title: Histone ChIP-seq from spleen (ENCLB165UIE)

description:
https://www.encodeproject.org/experiments/ENCSR928BGP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR928BGP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB165UIE
fragmentation methods: sonication (generic)
size range: 200-600


title: Normal 9

description: processed data file: all.rpkm.txt

value: normal gallbladder


title: Nucleus Oprm1-Cre:H2BG Mu_P13

city: Stockholm

institute: Karolinska Institutet


title: Normal 10

description: processed data file: all.rpkm.txt


title: Nucleus Oprm1-Cre:H2BG Mu_P11


title: Normal 8

description: processed data file: all.rpkm.txt


title: Histone ChIP-seq from spleen (ENCLB371VAR)

description:
https://www.encodeproject.org/experiments/ENCSR928BGP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR928BGP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB371VAR
fragmentation methods: sonication (generic)
size range: 200-600


title: Normal 7

description: processed data file: all.rpkm.txt


title: Tumor 8

description: processed data file: all.rpkm.txt


title: Histone ChIP-seq from right atrium auricular region (ENCLB956CBC)

description:
https://www.encodeproject.org/experiments/ENCSR459CKR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR459CKR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB956CBC
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) right atrium auricular region tissue

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS524KBT at ENCODE; https://www.encodeproject.org/ENCBS524KBT/


title: Nucleus Oprm1-Cre:H2BG Mu_P10

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_P5


title: Nucleus Oprm1-Cre:H2BG Mu_P6


title: Tumor 7

description: processed data file: all.rpkm.txt


title: Nucleus Oprm1-Cre:H2BG Mu_P7


title: Nucleus Oprm1-Cre:H2BG Mu_P12


title: Histone ChIP-seq from tibial artery (ENCLB919PXQ)

description:
https://www.encodeproject.org/experiments/ENCSR923DBA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR923DBA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB919PXQ
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens male adult (37 years) tibial artery tissue

value: tibial artery

value: tissue

value: EnTEX:Artery - Tibial

value: male

value: adult

value: ENCBS452GMG at ENCODE; https://www.encodeproject.org/ENCBS452GMG/


title: Histone ChIP-seq from Peyer's patch (ENCLB557YMJ)

description:
https://www.encodeproject.org/experiments/ENCSR416ZMW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR416ZMW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR708OCZ
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB557YMJ
fragmentation methods: sonication (generic)
size range: 200-600

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum updated Feb 2019 with updated term name and ID from DCC.

value: 37 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS388XLV at ENCODE; https://www.encodeproject.org/ENCBS388XLV/


title: Nucleus Oprm1-Cre:H2BG Mu_P8


title: Nucleus Oprm1-Cre:H2BG Mu_P9


title: Tumor 6

description: processed data file: all.rpkm.txt

value: gallbladder cancer

value: gallbladder tumor


title: Histone ChIP-seq from Peyer's patch (ENCLB962SQB)

description:
https://www.encodeproject.org/experiments/ENCSR416ZMW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR416ZMW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR708OCZ
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB962SQB
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_P3


title: Normal 5

description: processed data file: all.rpkm.txt

value: normal gallbladder


title: Nucleus Oprm1-Cre:H2BG Mu_P4

value: untreated


title: Histone ChIP-seq from tibial artery (ENCLB256OCS)

description:
https://www.encodeproject.org/experiments/ENCSR923DBA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR923DBA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB256OCS
fragmentation methods: none
size range: 200-600

value: tibial artery


title: Histone ChIP-seq from tibial artery (ENCLB724EKH)

description:
https://www.encodeproject.org/experiments/ENCSR891BTJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR891BTJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB724EKH
fragmentation methods: none
size range: 200-600

value: tissue


title: Tumor 5

description: processed data file: all.rpkm.txt


title: Nucleus Oprm1-Cre:H2BG Mu_O24


title: Nucleus Oprm1-Cre:H2BG Mu_P2


title: PDMC_IBMX_0hr_rep2

description: 0.4 mM IBMX

source_name: PDMC, IBMX, 0hr, replicate 2

value: female

value: placenta

tag: differentiation status

value: undifferentiated


title: Histone ChIP-seq from tibial artery (ENCLB307UGU)

description:
https://www.encodeproject.org/experiments/ENCSR891BTJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR891BTJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB307UGU
fragmentation methods: none
size range: 200-600

value: EnTEX:Artery - Tibial

value: male

value: adult

value: ENCBS452GMG at ENCODE; https://www.encodeproject.org/ENCBS452GMG/


title: Nucleus Oprm1-Cre:H2BG Mu_O23


title: Histone ChIP-seq from suprapubic skin (ENCLB625JSM)

description:
https://www.encodeproject.org/experiments/ENCSR413QLR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR413QLR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB625JSM
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) suprapubic skin tissue

value: suprapubic skin

value: EnTEX:Skin - Not Sun Exposed (Suprapubic) updated Feb 2019 with updated term name and ID from DCC.

value: 37 year

value: Bradley Bernstein, Broad

value: ENCBS874KYB at ENCODE; https://www.encodeproject.org/ENCBS874KYB/


title: Normal 6

description: processed data file: all.rpkm.txt

value: gallbladder cancer


title: Nucleus Oprm1-Cre:H2BG Mu_O22


title: Normal 4

description: processed data file: all.rpkm.txt

value: normal gallbladder


title: Nucleus Oprm1-Cre:H2BG Mu_O20

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_O21


title: Histone ChIP-seq from suprapubic skin (ENCLB724AVZ)

description:
https://www.encodeproject.org/experiments/ENCSR413QLR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR413QLR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB724AVZ
fragmentation methods: sonication (generic)
size range: 200-600

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Normal 3

description: processed data file: all.rpkm.txt


title: Nucleus Oprm1-Cre:H2BG Mu_O18


title: Tumor 4

description: processed data file: all.rpkm.txt

value: gallbladder tumor


title: Nucleus Oprm1-Cre:H2BG Mu_O17


title: Nucleus Oprm1-Cre:H2BG Mu_O16